New module staphscan

modules/nf-core/staphscan/environment.yml

@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::staphscan=0.3.1

modules/nf-core/staphscan/main.nf

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+process STAPHSCAN {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/staphscan:0.3.1--pyhdfd78af_0' :
+        'quay.io/biocontainers/staphscan:0.3.1--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fastas)
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: tsv
+    path "versions.yml", topic: versions, emit: versions_staphscan
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    staphscan \\
+        $args \\
+        -o ${prefix}_outdir \\
+        --report ${prefix}_summary.tsv \\
+        -i $fastas
+    mv ${prefix}_outdir/*.tsv . || true
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        staphscan: \$( echo \$(staphscan --version | sed 's/staphscan v//;'))
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_summary.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        staphscan: \$( echo \$(staphscan --version | sed 's/staphscan v//;'))
+    END_VERSIONS
+    """
+}

modules/nf-core/staphscan/meta.yml

@@ -0,0 +1,67 @@
+name: staphscan
+description: staphscan is a tool to screen genome assemblies of Staphylococcus
+  aureus
+keywords:
+  - screen
+  - assembly
+  - Staphylococcus
+  - aureus
+tools:
+  - staphscan:
+      description: a genomic surveillance framework for Staphylococcus aureus
+      homepage: https://github.com/riccabolla/StaphSCAN
+      documentation: https://staphscan.readthedocs.io/en/latest/
+      tool_dev_url: https://github.com/riccabolla/StaphSCAN
+      doi: 10.5281/zenodo.18458858
+      licence:
+        - "MIT"
+      identifier: biotools:staphscan
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fastas:
+        type: list
+        description: Staphylococcus aureus genome assemblies to be screened
+        pattern: "*.fasta"
+output:
+  tsv:
+    - - meta:
+          type: string
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.tsv":
+          type: file
+          description: Result file generated after screening
+          pattern: "*.tsv"
+          ontologies:
+            - edam: http://edamontology.org/format_3475
+  versions_staphscan:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750
+topics:
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750
+authors:
+  - "@riccabolla"
+maintainers:
+  - "@riccabolla"
+versions_staphscan:
+  - - versions.yml: null
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+      ontologies:
+        - edam: http://edamontology.org/format_3750

modules/nf-core/staphscan/tests/main.nf.test

@@ -0,0 +1,65 @@
+
+nextflow_process {
+
+    name "Test Process STAPHSCAN"
+    script "../main.nf"
+    process "STAPHSCAN"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "staphscan"
+
+    test("test-staphscan") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+				        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true),
+				        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/scaffolds.fasta', checkIfExists: true)
+				    ]
+                ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
+
+    test("test-staphscan-stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+				        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true),
+				        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/scaffolds.fasta', checkIfExists: true)
+				    ]
+                ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/staphscan/tests/main.nf.test.snap

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+{
+    "test-staphscan": {
+        "content": [
+            {
+                "tsv": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_summary.tsv:md5,c13d6d7e15052d80610185e3546113bd"
+                    ]
+                ],
+                "versions_staphscan": [
+                    "versions.yml:md5,b5af7928d06c090353c94a54c70f1672"
+                ]
+            }
+        ],
+        "timestamp": "2026-05-09T15:21:42.171023636",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
+    },
+    "test-staphscan-stub": {
+        "content": [
+            {
+                "tsv": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_staphscan": [
+                    "versions.yml:md5,b5af7928d06c090353c94a54c70f1672"
+                ]
+            }
+        ],
+        "timestamp": "2026-05-09T15:31:04.888855131",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
+    }
+}